Sequencing Study Detects Recombination of MERS

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   Sequencing Study Detects Recombination of MERS Coronavirus on Route to China

Sep 10, 2015

a GenomeWeb staff reporter

NEW YORK (GenomeWeb) – The Middle Eastern respiratory syndrome coronavirus (MERS-CoV) appears to have recombined prior to being introduced to China earlier this year, according to a genomic and phylogenetic analysis published in mBio this week.

A team led by investigators at the Chinese Center for Disease Control and Prevention sequenced the genome of a MERS-CoV strain dubbed ChinaGD01 that was introduced to China in May after first reaching South Korea, where a Korean man returned home ill after visiting four Middle Eastern countries. A handful of his relatives subsequently contracted the virus, as did an individual who visited the man's father in the hospital before traveling to China later that month.

Based on the genome sequence data and phylogenetic comparisons with other characterized MERS-CoV strains, the researchers concluded that the Chinese and South Korean MERS-CoV strain resulted from recombination between MERS viruses from two clade B groups, which likely took place in mid to late 2014.

"Based on the latest genome sequences from South Korea and the Kingdom of Saudi Arabia, our research indicated that a novel type of genetic recombination has occurred in the MERS-CoV strain prevalent in South Korea," senior authors Wenjie Tan and George Gao, at the Chinese Center for Disease Control and Prevention, and their colleagues wrote.

Since its discovery in 2012, MERS-CoV has been linked to often deadly respiratory tract infections in Saudi Arabia and beyond, affecting more than 1,300 people. And over the past several months, the team noted, South Korea has experienced the largest MERS-CoV outbreak outside of the Middle East so far, with nearly 200 infections and at least 36 deaths.

Using a combination of Ion Torrent and Sanger sequencing technology, the researchers analyzed the RNA found in nasopharyngeal swabs from a 44-year-old Korean man who had been in contact with some of the first infected individuals in South Korea and was diagnosed with MERS-CoV at a hospital in Guangdong province in China.

After tossing out human reads, they used a CLC Genomic workflow to put together a 30,144-base viral genome assembly that is believed to span the full length of the Chinese MERS-CoV strain ChinaGD01.

The team then compared this sequence to previously sequenced MERS-CoV strains, uncovering variants that differentiate it from strains in South Korea and Saudi Arabia.

The researchers' initial phylogenetic analysis, based on whole-genome sequences for the available strains, suggested ChinaGD01 fits into group 3 in the MERS-CoV clade, known as clade B. So, too, did an analysis focused on the MERS-CoV open reading frames ORF1a and ORF1b.

Nevertheless, when the team focused on S gene segment similarities, it saw signs of clustering with clade B's group 5, suggesting ChinaGD01 is the product of recombination between group 3 and group 5 MERS viruses — a notion confirmed through subsequent SNP and other analyses.

The recombination in question appears to have occurred sometime in the second half of 2014, the researchers reported, producing a strain that resembles those found recently in Saudi Arabia and South Korea.

"We note that six MERS-CoV isolates from 2015 (ChinaGD01, the first MERS-CoV strain from South Korea, and the four latest strains from Saudi Arabia) had high levels of nucleotide identity … and showed the same recombination signal in our analyses," the authors of the study concluded.

"However, more studies are needed to understand the relationship between genetic recombination of MERS-CoV, the biological properties it conveys, and its relevance to the recent high rate of transmission," they explained.

In a related mBio commentary, Columbia University's Ian Lipkin noted that coronaviruses such as MERS-CoV are known for their recombination capabilities and said it "would not be surprising … if recombination were to occur in MERS-CoV and to result in enhanced transmission or virulence."

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arirish Members Profile Send Private Message Find Members Posts Add to Buddy List Admin Group Joined: June 19 2013 Location: Arkansas Status: Offline Points: 39215	Post Options Post Reply Quote arirish Report Post Thanks(0) Quote Reply Topic: Sequencing Study Detects Recombination of MERS Posted: September 10 2015 at 11:13am
	Sequencing Study Detects Recombination of MERS Coronavirus on Route to China Sep 10, 2015 a GenomeWeb staff reporter NEW YORK (GenomeWeb) – The Middle Eastern respiratory syndrome coronavirus (MERS-CoV) appears to have recombined prior to being introduced to China earlier this year, according to a genomic and phylogenetic analysis published in mBio this week. A team led by investigators at the Chinese Center for Disease Control and Prevention sequenced the genome of a MERS-CoV strain dubbed ChinaGD01 that was introduced to China in May after first reaching South Korea, where a Korean man returned home ill after visiting four Middle Eastern countries. A handful of his relatives subsequently contracted the virus, as did an individual who visited the man's father in the hospital before traveling to China later that month. Based on the genome sequence data and phylogenetic comparisons with other characterized MERS-CoV strains, the researchers concluded that the Chinese and South Korean MERS-CoV strain resulted from recombination between MERS viruses from two clade B groups, which likely took place in mid to late 2014. "Based on the latest genome sequences from South Korea and the Kingdom of Saudi Arabia, our research indicated that a novel type of genetic recombination has occurred in the MERS-CoV strain prevalent in South Korea," senior authors Wenjie Tan and George Gao, at the Chinese Center for Disease Control and Prevention, and their colleagues wrote. Since its discovery in 2012, MERS-CoV has been linked to often deadly respiratory tract infections in Saudi Arabia and beyond, affecting more than 1,300 people. And over the past several months, the team noted, South Korea has experienced the largest MERS-CoV outbreak outside of the Middle East so far, with nearly 200 infections and at least 36 deaths. Using a combination of Ion Torrent and Sanger sequencing technology, the researchers analyzed the RNA found in nasopharyngeal swabs from a 44-year-old Korean man who had been in contact with some of the first infected individuals in South Korea and was diagnosed with MERS-CoV at a hospital in Guangdong province in China. After tossing out human reads, they used a CLC Genomic workflow to put together a 30,144-base viral genome assembly that is believed to span the full length of the Chinese MERS-CoV strain ChinaGD01. The team then compared this sequence to previously sequenced MERS-CoV strains, uncovering variants that differentiate it from strains in South Korea and Saudi Arabia. The researchers' initial phylogenetic analysis, based on whole-genome sequences for the available strains, suggested ChinaGD01 fits into group 3 in the MERS-CoV clade, known as clade B. So, too, did an analysis focused on the MERS-CoV open reading frames ORF1a and ORF1b. Nevertheless, when the team focused on S gene segment similarities, it saw signs of clustering with clade B's group 5, suggesting ChinaGD01 is the product of recombination between group 3 and group 5 MERS viruses — a notion confirmed through subsequent SNP and other analyses. The recombination in question appears to have occurred sometime in the second half of 2014, the researchers reported, producing a strain that resembles those found recently in Saudi Arabia and South Korea. "We note that six MERS-CoV isolates from 2015 (ChinaGD01, the first MERS-CoV strain from South Korea, and the four latest strains from Saudi Arabia) had high levels of nucleotide identity … and showed the same recombination signal in our analyses," the authors of the study concluded. "However, more studies are needed to understand the relationship between genetic recombination of MERS-CoV, the biological properties it conveys, and its relevance to the recent high rate of transmission," they explained. In a related mBio commentary, Columbia University's Ian Lipkin noted that coronaviruses such as MERS-CoV are known for their recombination capabilities and said it "would not be surprising … if recombination were to occur in MERS-CoV and to result in enhanced transmission or virulence."
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arirish Members Profile Send Private Message Find Members Posts Add to Buddy List Admin Group Joined: June 19 2013 Location: Arkansas Status: Offline Points: 39215	Post Options Post Reply Quote arirish Report Post Thanks(0) Quote Reply Posted: September 10 2015 at 11:58am
	As Saudi MERS total grows, study hints at increased transmissibility Saudi Arabia's government today reported two more MERS-CoV infections, one involving a healthcare worker likely infected in Riyadh's outbreak, and Chinese researchers detailed a comparison of recent samples that hints at increased transmissibility. In other developments, the Saudi agriculture ministry announced new results from a large camel sampling project, which revealed that 3.3% of the country's animals are probably infected with MERS-CoV (Middle East respiratory syndrome coronavirus). Two new cases, 1 death One of the latest lab-confirmed cases involves a 25-year-old male Saudi healthcare worker in Riyadh whose contact with a suspected or confirmed MERS case is under review, the country's Ministry of Health (MOH) said in a statement. The man is hospitalized in critical condition. His illness is likely part of an ongoing hospital outbreak in Riyadh. It's not known how many cases are linked to the health setting, but 159 infections in the city have been reported since Jul 21. Also, the WHO's statements since the third week of August have acknowledged 77 hospital-linked cases. The second case involves a 61-year-old Saudi man from Dawadmi, located about 200 miles west of Riyadh. The patient is listed in stable condition and didn't have any known contact with another MERS-CoV patient. As of today, 58 people in Saudi Arabia—where cases have also been reported in several other cities—are still being treated for their infections. Another 13 are in home isolation. The MOH said six more people have recovered from MERS-CoV, two of them healthcare workers from other countries who may be two Filipino nurses discharged from the hospital who were described by the Philippines media. Citing a Philippines government official, the Manila Times reported yesterday that two nurses, a male and a female, have recovered and two more nurses are still hospitalized in serious condition but show signs of improvement. The story said 10 Filipino health workers have been infected with MERS-CoV, 8 in Saudi Arabia and 2 in the United Arab Emirates. One more death was reported in a previously announced patient, the MOH said, involving a 41-year-old Saudi man who had an underlying health condition. Today's developments lift Saudi Arabia's totals from the disease to 1,225 cases, 521 of them fatal. Since the virus emerged in Saudi Arabia in 2012, 633 MERS patients have recovered. Study finds recombination evidence A research team from China that conducted full-genome sequencing of a sample from the country's imported MERS-CoV case, detected in May in a traveler from South Korea, found amino acid changes and evidence of a fairly recent recombination event. The investigators said the changes could have played a role in enhanced human-to-human spread in South Korea's hospital outbreak. The team, writing yesterday in mBio, based its findings on a comparison of the sample with other recent viruses from South Korea and Saudi Arabia. In early June, preliminary sequencing of samples from China and South Korea by an international group of collaborators found that the MERS viruses clustered with viruses collected earlier this year from a Riyadh outbreak, with hints that the ones in the Asian travelers could have resulted from a separate zoonotic event somewhere in the Arabian Peninsula. That earlier analysis suggested that the samples weren't likely to have differences in virulence and transmissibility when compared with MERS-CoV circulating in the Middle East, though the researchers said that more clinical, epidemiologic, and genetic data would be needed to confirm the findings. In the new, more detailed look at genes from the viruses, the Chinese team found 11 amino acid substitutions in the sample from the South Korean man in China, 8 that were shared with the strain collected in South Korea and those circulating recently in Saudi Arabia. Their analysis suggested that the viruses from China and South Korea reflect a recombination pattern that was also seen in recent MERS-CoV cases in Saudi Arabia, and they estimated that recombination occurred in Saudi Arabia at the end of 2014. In a commentary in the same issue of mBio, W. Ian Lipkin, MD, director of the Center for Infection and Immunity at Columbia University's Mailman School of Public Health, said that recombination is common in coronaviruses and it wouldn't be surprising if it occurred with MERS-CoV in a way that enhanced transmission or virulence. He said the findings are important, because they point to a possible recombination event that may have produced a new lineage of MERS-CoV that has different transmission properties, but added that more epidemiologic and lab studies are needed to confirm the virus changes. Camel sampling results An official from Saudi Arabia's Ministry of Agriculture unveiled the results of a camel sampling at a Sep 7 media briefing in Riyadh, and said the findings provider stronger proof that camels are transmitting the virus to people, Arab News reported today. Bats and camels are thought to harbor the virus, but the animal reservoir and intermediate sources of the virus haven't been fully defined. Ibrahim Qassem, director general of the ministry's livestock division, said 40 survey teams that included 200 veterinarians looked at 32,000 samples from 8,000 camels. They found that 81.5% of the animals were immune to the virus and 3.3% carry or spread it, according to the news report. He estimated that 7,700 of the country's 233,000 camels are infected with MERS-CoV. Qassem told reporters that although the findings confirm the relationship between camels and the virus, they aren't likely to settle the debate about transmission from camels to people. He added that the ministry is trying to determine how camels are infected and if they are infected by other animals. http://www.cidrap.umn.edu/news-perspective/2015/09/saudi-mers-total-grows-study-hints-increased-transmissibility
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